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At least 991 records · Page 55Linked to original sources
PubMed1995

On the solution of the molecular-replacement problem at very low resolution: application to large complexes.

The applicability of the molecular-replacement (MR) method, implemented through the AMoRe package [Navaza (1994). Acta Cryst. A50, 157-163], is studied at very low resolution (d > 20 A) and for very large molecular complexes. Due to the nature of the low-resolution data, specific problems appear. In particular, rotation-function peaks are very broad and translation functions based on Patterson overlap show large spurious peaks. To solve these problems, the translation function is replaced by a search using amplitude correlation and a systematic three-dimensional angular search is performed around each rotation-function peak. Furthermore, these functions are applied in different resolution ranges during the same search. The corresponding algorithms are applied to two cases: the tRNA(Asp)-synthetase complex (neutron diffraction data) and a ribosome model crystal (calculated data). This new implementation is shown to solve the problem for a variety of search models, ranging from a detailed atomic model to a rough envelope.

Journal Article↗
PubMed1999

The geometry of metal-ligand interactions relevant to proteins.

Geometrical data which could be of relevance in the structure determination, structure refinement, assessment or understanding of metalloproteins have been extracted from the Cambridge Structural Database (CSD). The CSD contains crystallographic data from 'small-molecule' structures determined by X-ray or neutron diffraction to an accuracy much better than that of most current protein structure determinations. The structures selected have a crystallographic R factor </= 0.065 and contain Ca, Mg, Mn, Fe, Cu or Zn interacting with ligands which are analogues of the amino-acid side chains commonly found in proteins; they include carboxylate groups, alcohols, phenolates, thiolates, imidazole groups and also water molecules. For each pair, the mean metal-donor-atom distance, the sample standard deviation and the range of observed values are tabulated, using approximately 4500 observations in all. Where practicable, subsets with different coordination numbers and/or oxidation states are given. Also included are inter-bond angles at the ligand donor atom, the orientation of carboxylate and imidazole groups with respect to the metal-donor-atom bond and some other aspects of ligand geometry. Thus, for example, target distances and their standard deviations could be easily looked up for the validation of a metalloprotein structure or for use in restrained refinement with low-resolution data.

Carboxylic Acids↗
PubMed2001

Liquid Rb micrometric droplets confined in paraffin wax: an X-ray absorption spectroscopy study.

We have performed high-quality X-ray absorption measurements on crystalline (c-Rb) and liquid (l-Rb) Rubidium in the range from 15 K to 320 K. Performing a consistent analysis that takes into account the contribution of the medium range structure, we observe that the l-Rb spectrum is compatible with pair correlation function g(r) previously determined by neutron diffraction experiments. Due to the micrometric size of the liquid droplets we were able to observe a slight undercooling down to 290 K. We were also able to study the details of the very strong multielectron excitations channels in terms of resonances, edges and shake-off features at proper theoretical energy values.

Journal Article↗
PubMed2006

Positioning of proteins in membranes: a computational approach.

A new computational approach has been developed to determine the spatial arrangement of proteins in membranes by minimizing their transfer energies from water to the lipid bilayer. The membrane hydrocarbon core was approximated as a planar slab of adjustable thickness with decadiene-like interior and interfacial polarity profiles derived from published EPR studies. Applicability and accuracy of the method was verified for a set of 24 transmembrane proteins whose orientations in membranes have been studied by spin-labeling, chemical modification, fluorescence, ATR FTIR, NMR, cryo-microscopy, and neutron diffraction. Subsequently, the optimal rotational and translational positions were calculated for 109 transmembrane, five integral monotopic and 27 peripheral protein complexes with known 3D structures. This method can reliably distinguish transmembrane and integral monotopic proteins from water-soluble proteins based on their transfer energies and membrane penetration depths. The accuracies of calculated hydrophobic thicknesses and tilt angles were approximately 1 A and 2 degrees, respectively, judging from their deviations in different crystal forms of the same proteins. The hydrophobic thicknesses of transmembrane proteins ranged from 21.1 to 43.8 A depending on the type of biological membrane, while their tilt angles with respect to the bilayer normal varied from zero in symmetric complexes to 26 degrees in asymmetric structures. Calculated hydrophobic boundaries of proteins are located approximately 5 A lower than lipid phosphates and correspond to the zero membrane depth parameter of spin-labeled residues. Coordinates of all studied proteins with their membrane boundaries can be found in the Orientations of Proteins in Membranes (OPM) database:http://opm.phar.umich.edu/.

Amino Acids↗
PubMed1982

Static and time-resolved structural studies of the Ca2+-ATPase of isolated sarcoplasmic reticulum.

X-ray and neutron diffraction studies of oriented multilayers of isolated light sarcoplasmic reticulum (SR) have provided the separate profile structures of the lipid bilayer and the Ca2+-ATPase molecule within the membrane profile to approximately 10 A resolution. These studies utilized biosynthetically deuterated SR phospholipids incorporated isomorphously into the isolated SR membranes via exchange proteins. Time-resolved x-ray diffraction studies of these oriented SR membrane multilayers have indicated that significant changes occur in the membrane profile structure within a single turnover of the Ca2+-transport cycle. These studies utilized the flash photolysis of caged ATP to effectively synchronize the ensemble of Ca2+-ATPase molecules in the multilayer, synchrotron x-radiation to provide 100- to 500-millisecond data collection times, and double-beam spectrophotometry to monitor Ca2+ transport in the oriented SR membrane multilayer.

Animals↗
PubMed1991

Molecular details of anesthetic-lipid interaction.

By means of isotopic labeling with deuterium (2H) and observation by nuclear magnetic resonance (NMR), it has been possible to measure the conformational ordering and dynamics of lipids and anesthetics in membranes. The local anesthetic tetracaine causes disordering in the acyl chains of the lipids, very little effect near the glyceryl residue, and minor ordering effects in the charged head group. The anesthetic itself is well ordered within the lipid matrix. The magnitudes of these effects depend upon the nature of the lipid, and upon whether or not the anesthetic is charged. A model can be constructed for the location of the anesthetic within the lipid bilayers. Confirmation of the model comes from Fourier transform infrared spectroscopy (FTIR), which also shows directly the pressure-driven exclusion of local anesthetic from lipid, and the augmentation of this effect by the presence of cholesterol. Future studies by solid-state NMR of protein, and neutron diffraction of specifically deuterated components of anesthetic-nerve systems, should reveal even more precise details of the molecular events involved in anesthesia.

Anesthesia↗
PubMed2006

The preparation and structures of hydrogen ordered phases of ice.

Two hydrogen ordered phases of ice were prepared by cooling the hydrogen disordered ices V and XII under pressure. Previous attempts to unlock the geometrical frustration in hydrogen-bonded structures have focused on doping with potassium hydroxide and have had success in partially increasing the hydrogen ordering in hexagonal ice I (ice Ih). By doping ices V and XII with hydrochloric acid, we have prepared ice XIII and ice XIV, and we analyzed their structures by powder neutron diffraction. The use of hydrogen chloride to release geometrical frustration opens up the possibility of completing the phase diagram of ice.

Journal Article↗
PubMed1991

NMR studies of the structure and dynamics of membrane-bound bacteriophage Pf1 coat protein.

Filamentous bacteriophage coat protein undergoes a remarkable structural transition during the viral assembly process as it is transferred from the membrane environment of the cell, where it spans the phospholipid bilayer, to the newly extruded virus particles. Nuclear magnetic resonance (NMR) studies show the membrane-bound form of the 46-residue Pf1 coat protein to be surprisingly complex with five distinct regions. The secondary structure consists of a long hydrophobic helix (residues 19 to 42) that spans the bilayer and a short amphipathic helix (residues 6 to 13) parallel to the plane of the bilayer. The NH2-terminus (residues 1 to 5), the COOH-terminus (residues 43 to 46), and residues 14 to 18 connecting the two helices are mobile. By comparing the structure and dynamics of the membrane-bound coat protein with that of the viral form as determined by NMR and neutron diffraction, essential features of assembly process can be identified.

Capsid↗
PubMed1997

Compressibility, Phase Transitions, and Oxygen Migration in Zirconium Tungstate, ZrW2O8

In situ neutron diffraction experiments show that at pressures above 2 kilobars, cubic zirconium tungstate (ZrW2O8) undergoes a quenchable phase transition to an orthorhombic phase, the structure of which has been solved from powder diffraction data. This phase transition can be reversed by heating at 393 kelvin and 1 atmosphere and involves the migration of oxygen atoms in the lattice. The high-pressure phase shows negative thermal expansion from 20 to 300 kelvin. The relative thermal expansion and compressibilities of the cubic and orthorhombic forms can be explained in terms of the "cross-bracing" between polyhedra that occurs as a result of the phase transition.

Journal Article↗
PubMed2001

First solvation shell of the Cu(II) aqua ion: evidence for fivefold coordination.

We determined the structure of the hydrated Cu(II) complex by both neutron diffraction and first-principles molecular dynamics. In contrast with the generally accepted picture, which assumes an octahedrally solvated Cu(II) ion, our experimental and theoretical results favor fivefold coordination. The simulation reveals that the solvated complex undergoes frequent transformations between square pyramidal and trigonal bipyramidal configurations. We argue that this picture is also consistent with experimental data obtained previously by visible near-infrared absorption, x-ray absorption near-edge structure, and nuclear magnetic resonance methods. The preference of the Cu(II) ion for fivefold instead of sixfold coordination, which occurs for other cations of comparable charge and size, results from a Jahn-Teller destabilization of the octahedral complex.

Journal Article↗
PubMed2003

Solid state polymorphism of liquid crystals in confined geometries.

Solid polymorphism of 4-alkyl-4'-cyanobiphenyl (nCB) was studied so far as a function of thermal history. In this paper we show that metastable solid phases of 4-octyl-4'-cyanobiphenyl (8CB) are also formed when the mesogens are confined in porous silica matrices and we study their structure by neutron diffraction and by Raman spectroscopy. Three metastable solid states are identified: one crystalline phase K', two frozen-in smectic-like phases K(s) and K'(s). We discuss the relation between the structure of the metastable solid phases and that of the mesomorph phases.

Journal Article↗
PubMed2006

Influence of hydration on the dynamics of lysozyme.

Quasielastic neutron and light-scattering techniques along with molecular dynamics simulations were employed to study the influence of hydration on the internal dynamics of lysozyme. We identified three major relaxation processes that contribute to the observed dynamics in the picosecond to nanosecond time range: 1), fluctuations of methyl groups; 2), fast picosecond relaxation; and 3), a slow relaxation process. A low-temperature onset of anharmonicity at T approximately 100 K is ascribed to methyl-group dynamics that is not sensitive to hydration level. The increase of hydration level seems to first increase the fast relaxation process and then activate the slow relaxation process at h approximately 0.2. The quasielastic scattering intensity associated with the slow process increases sharply with an increase of hydration to above h approximately 0.2. Activation of the slow process is responsible for the dynamical transition at T approximately 200 K. The dependence of the slow process on hydration correlates with the hydration dependence of the enzymatic activity of lysozyme, whereas the dependence of the fast process seems to correlate with the hydration dependence of hydrogen exchange of lysozyme.

Animals↗
PubMed2003

The structure of the Ca2+-ATPase of sarcoplasmic reticulum.

In this article the morphology of sarcoplasmic reticulum, classification of Ca(2+)-ATPase (SERCA) isoenzymes presented in this membrane system, as well as their topology will be reviewed. The focus is on the structure and interactions of Ca(2+)-ATPase determined by electron and X-ray crystallography, lamellar X-ray and neutron diffraction analysis of the profile structure of Ca(2+)-ATPase in sarcoplasmic reticulum multilayers. In addition, targeting of the Ca(2+)-ATPase to the sarcoplasmic reticulum is discussed.

Amino Acid Sequence↗
PubMed1992

[System of crystal structure analysis on pc computer--NOMCSDP package].

The package of crystal structure analysis--NOMCSDP (Natural Organic Molecule Crystal Structure Determination Package) Version 1.0 has been developed on the widely used IBM PC computer. It can perform the whole task of X-ray crystal structure analysis, as well as can be used for computing crystal structure on neutron diffraction. NOMCSDP has many advantages--easy operation, less needs for specialized crystallographic knowledge, wide applicability of solving structure, and having all the necessary functions. The inexorable trend of X-ray crystal structure analysis in the course of realizing the wide spread use in determining molecular structure of natural products was discussed and the practical uses of NOMCSDP were illustrated with examples. We hope that this version will play active role in the process of promoting routine use of crystal structure analysis.

Crystallization↗
PubMed1990

The "microassembly" of integral membrane proteins: applications & implications.

We summarize some evidence in favor of the view that the transmembrane region of many, perhaps most integral membrane proteins is made up of an aggregate of hydrophobic alpha-helices, each of which behaves as an autonomous folding domain. Folding of these proteins is seen as a two-stage process during which individual transmembrane helices first form in response to local interactions between the polypeptide and the aqueous and lipid phases, and then pack without extensive rearrangement to yield the three-dimensional structure. This two-stage model is supported by examination of those few structures that are known to a sufficient resolution, by experiments in which functional integral membrane proteins are "microassembled" from separately folded fragments, and by the existence in the inner membranes of organelles of a large number of very small integral subunits, often barely longer than a single transmembrane alpha-helix. We describe application of microassembly to establishing the path of the polypeptide in the tertiary structure of bacteriorhodopsin by neutron diffraction and we briefly discuss its possible role in the biosynthesis of organelle inner membrane complexes and its implications for model building from sequence data.

Amino Acid Sequence↗
PubMed1985

Texture, stress and age in the human femur.

The way in which remodelling of human bone is determined by the mechanics of life is explored in a neutron diffraction study of the femur. The hydroxyapatite crystals provide ability to resist vertical stress by a preferred alignment which is low at birth, increases to a maximum at an age of about three years and then falls away steadily in later life. This vertical alignment is greater at the front of the femur than at the back.

Adolescent↗
PubMed1994

Constraint satisfaction techniques for modeling large complexes: application to the central domain of 16S ribosomal RNA.

Standard experimental techniques for determining the structure of small to moderately-sized molecules are difficult to apply to large macromolecular complexes. These complexes, consisting of multiple protein and/or nucleic acid components, can contain many thousands of atoms and the experimental techniques used to study them provide relatively sparse structural information with significant measurement uncertainty. Computational technologies are required to reduce the conformational search space and synthesize the data in order to produce the structures or (more usually) sets of structures compatible with the data. In this paper, we show that a method based on the constraint satisfaction paradigm produces a three-dimensional topology for the central domain of the 16S ribosomal RNA that is generally consistent with interactively built models, although differing in significant ways. The modeling incorporates information about secondary structure of the nucleic acid, neutron diffraction data about the relative positions and uncertainties of the proteins, and protection experiments indicating proximities of segments of RNA to specific protein subunits. Unlike previously proposed models, our model contains explicit information about the range of positions for each subunit that are compatible with the data. The system uses a grid search, checks distances in a direction-dependent manner, uses disjunctive distance constraints, and checks for volume overlap violations.

Animals↗